Matrix proteins exist in the biomineralization microstructure of shells and pearls. Calcium carbonate forms the high regular and complex biomineralization microstructure under the influence of matrix proteins. It is important to study the matrix proteins in the shells and pearls of the cultured pearl bivalves for the understanding of the mechanism of the pearl formation. This paper reviews the matrix proteins which had been found and studied, their structure and function in biomineralization, and current research progress of the understanding of the mechanism of the pearl formation with the knowledge of matrix proteins.